Research involving the analysis of gene information, as typified by the Human Genome Project, is occurring at an ever faster pace worldwide, bringing with it an increasing need for new methodologies capable of efficiently analyzing expressions at the in-vivo gene level.
A new method for measuring gene expression levels in cells is a DNA microarray, wherein several hundred to several tens of thousands of samples of DNA are aligned and fixed in spots in a matrix shape to a glass slide. mRNA (the target) that has been extracted and purified from target cells is hybridized on the DNA microarray.
Fundamentally, the common method for performing measurements using DNA microarrays is two-color fluorescence labeling. In this method, mRNA originating from two types of cells (for example, normal cells and cancer cells) is extracted and purified, and the cells are labeled with fluorescent materials (CY3 and CY5) that have mutually differing excitation wave lengths. Then, competitive hybridization is performed on the same spots on the DNA microarray, and the fluorescent intensity of each spot on the array is measured by using two channels (CH1 and CH2) to view the mutually differing excitation wave lengths CY3 and CY5. By this means, the comparative quantity of gene level expression of the two types of cells is measured. In practice, after the fluorescent signals have been measured, the measurement results are superposed and color analysis is performed.
The data from CY3 and CY5 is normally calculated based on the following relational expression, with essentially the value of log (R/G) being utilized as the gene expression data.
(Sample A CY3 fluorescence data)
    CH1–CH1B (Channel 1 background)=data R of CY3 (red)(Sample B CY5 fluorescence data)    CH2–CH2B (Channel 2 background)=data G of CY5 (green)
Here, CH1 (channel 1) and CH2 (channel 2) are the measured fluorescent intensity values of the spots (channel 1 and 2 existing so as to measure red and green separately), measured using a laser scanner. Further, CH1B (background data of channel 1) and CH2B (background data of channel 2) are background data of the spots measured using a laser scanner.
Gene spots with a greater degree of gene expression in Sample A show as red, spots with a greater degree of gene expression in Sample B show as green, and spots with an approximately equal degree of gene expression show as yellow. That is, the spots show the following colors, in accordance with the ratio of R to G:    R/G>1 Red    R/G=1 Yellow    R/G<1 Green
As research based on DNA microarray data, such as the analysis of periodicity between genes, gene expression networks, and gene transfer control cascades, is being developed, and mathematical informational methods of this second generation research crucially require improved accuracy. A high degree of reliability is required with respect to the data from DNA microarrays.
Further, highly accurate data is required in the case where cancer is diagnosed on the basis of gene expression data.
However, gene analysis using DNA microarrays has only recently begun, and there are many cases where the issue of reproducibility needs to be resolved.
In particular, it is known that printing, hybridization, processing of the slide surface, etc. readily causes changes in the shape and size of the spots, and that mechanical influences during the spotting process, such as the minute displacement, vibration, etc. of the printing pins or platform, readily cause changes in the position of the spots.
Although the uniformity of the spots on the DNA microarray is an important factor that affects the accuracy of signal data, a method for evaluating this uniformity does not exist.
The present invention presents an extremely simple method for evaluating the uniformity of the spots on an array such as a DNA microarray, etc.